Lightroom Doesn't See Images on SD Card

Hi
Just come back from a photo trip and tried to import my images into Lightroom from my SD Card and Lightroom doesn't see them, all it see's are the images I took on Saturday.
Today I arrived at my location to photograph Pasque Flowers, I took 1 image then realised I hadn't deleted the images from Saturday so I used the 'Delete Images From Card' in my camera's menu and then proceeded to take a few hundred images. During the day I reviewed my images several times, so I know they were definitely saved to the SD Card.
When I got home I tried to import my images in to Lightroom and all Lightroom saw on the card were the images I took last Saturday.
I tried closing down Lightroom and opening it again - nothing, just the images from Saturday!
I tried using the SD Card reader on my iMac - again, just Saturday's images were found.
I then put my card back into my camera and all I could see were my Pasque flower images from today.
So it seems my camera see's todays images yet Lightroom only sees the images from Saturday I had deleted via my camera's menu at the start of today.
Does anyone have any ideas?
Regards
Chris
Lightroom 4.4
iMac 27"
Canon 5D MkIII
Lexar USB 2 Card Reader
Sandisk 16GB Extreme Pro SD Card

Hi Brett
Things have moved on today.
I have a long conversation with Canon and finally got the images off my camera by connecting it directly to my iMac and using Canon's EOS Utility to download the images. The EOS Utility saw both yesterdays images and the ones taken last Saturday.
I have to say it took several attempts to finally get all the images off the card and a similar number of attempts to get Lightroom to import them - but it has been achieved.
Interestingly the chap at Canon said that they (Canon) believe there is a problem with Lightroom's Library (not quite sure how I go about proving that). Anyway I have tried formatting the offending SD Card and none of the images are deleted which leads me to suspect, as you do that it might be a faulty SD card.
All the relevent serial numbers, invoice and photographs have been sent to Sandisk and I await their reply. Thankfully I purchased the card through Amazon UK who are the official retailer for Sandisk, so hopefully I should get my card replaced IF it is found to be faulty.

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I have a long conversation with Canon and finally got the images off my camera by connecting it directly to my iMac and using Canon's EOS Utility to download the images. The EOS Utility saw both yesterdays images and the ones taken last Saturday.
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